Abstract

Background

Vibrio campbellii is widely distributed in the marine environment and is an important pathogen of aquatic organisms such as shrimp, fish, and mollusks. An isolate of V. campbellii carrying the pirABvp gene, causing acute hepatopancreatic necrosis disease (AHPND), has been reported. There are no previous reports about the complete genome of V. campbellii causing AHPND (VCAHPND). To extend our understanding of the pathogenesis of VCAHPND at the genomic level, the genome of V. campbellii 20130629003S01 isolated from a shrimp with AHPND was sequenced and analysed.

Results

The complete genome sequence of V. campbellii 20130629003S01 was generated using the PacBio RSII platform with single molecule, real-time sequencing. The 20130629003S01 strain consists of two circular chromosomes (3,621,712 bp in chromosome 1 and 2,245,751 bp in chromosome 2) and four plasmids of 70,066, 204,531, 143,140, and 86,121 bp. The genome contains a total of 5855 protein coding genes, 134 tRNA genes and 37 rRNA genes. The average nucleotide identity value of 20130629003S01 and other reference V. campbellii strains was 97.46%, suggesting that they are closely related.

Conclusions

The genome sequence of V. campbellii 20130629003S01 and its comparative analysis with other V. campbellii strains that we present here are important for a better understanding of the genomic characteristics of VCAHPND.

Background

Vibrio campbellii is widely distributed in the marine environment and is an important pathogen of wild and reared marine organisms such as shrimp, fish, and mollusks [1]. In recent years, an isolate of V. campbellii carrying the pirABvp gene that causes acute hepatopancreatic necrosis disease (AHPND) has been reported [2]. Shrimp production in AHPND-affected regions (SE Asia and Mexico) has dropped sharply, which is causing heavy economic losses. Initially, V. parahaemolyticus, which becomes virulent by acquiring a unique extrachromosomal AHPND-associated plasmid carrying pirABvp (VPAHPND), was the only pathogen known to cause AHPND. Later, non-V. parahaemolyticus AHPND-causing Vibrio started emerging, and V. harveyi-like, V. owensii and V. campbellii strains have been reported [2,3,4].

Recent studies have shown that VPAHPND possesses not only toxin genes but also a ~70 kb plasmid, which expresses Pirvp [5]. However, there are no reports about the complete genome of V. campbellii that causes AHPND (VCAHPND). In this paper, we obtained the complete genome sequence of one strain of V. campbellii, which was isolated in June 2013 from the hepatopancreas of diseased Litopenaeus vannamei in Guangxi, China. PCR amplifications were performed using VpPirA and VpPirB primers specific to the pirABvp genes (pirAvp and pirBvp), and this strain was evaluated for its pathogenicity in L. vannamei [2]. The shrimp showed typical symptoms of AHPND, and cumulative mortalities reached 100% [2]. The genome sequencing of 20130629003S01 provides timely information for a better understanding of the genomic characteristics of the pathogen.

Methods

Genomic DNA isolation, sequencing and assembly

Strain 20130629003S01 is V. campbellii isolated in June 2013 from AHPND-affected L. vannamei in Guangxi, China. The genomic DNA of this strain was extracted using the Wizard Genomic DNA Purification Kit (Promega, Madison, WI, USA). The DNA was examined by 1% agarose gel electrophoresis and quantified using a NanoDrop 2000 spectrophotometer (Thermo Scientific, MA, USA). The genomic DNA was sequenced using the PacBio RSII platform by Majorbio Bio-Pharm Biotechnology Co., Ltd., Shanghai, China. A 10-kb DNA library was constructed according to the manufacturer’s protocols and sequenced using single-molecule real-time (SMRT) sequencing technology with P6-C4 chemistry. One SMART cell was used for sequencing, and the data were assembled de novo using the hierarchical genome assembly process (HGAP) [6]. The assembly was based on 1.02 Gb of PacBio data and polished with three successive passes through Quiver to reach a final consensus accuracy at 194× coverage. This assembly consisted of six contigs including two chromosomes and four plasmids. The repeat sequences at the end of the six contigs were removed to obtain the complete genome and plasmid sequences.

Genome annotation

Gene prediction was carried out using Glimmer [7], while rRNA and tRNA were analysed using RNAmmer [8] and tRNAscan-SE version 1.21 [9]. Gene annotation was carried out based on homology searches against the gene ontology (GO) database and clusters of orthologous groups (COG) protein database. Prophage regions were identified using the PHAge Search Tool (PHAST) [10]. Virulence genes were searched for using the virulence factor of pathogenic bacteria database (VFDB) [11] and BLAST.

Comparative genome analysis

The complete reference genome sequences of V. campbellii strains were downloaded from NCBI and used for comparative genome analysis. The accession numbers of the reference V. campbellii strains were DS40M4 (AGIE01000001–AGIE01000121), CAIM_519 (AMDG01000001–AMDG01000213), BAA-1116 (CP006605–CP006607), UMTGB204 (JSFE01000001–JSFE01000060), HY01 (DS179406–DS179608), LMB29 (CP019293–CP019298) and 051011E (BBKU01000001–BBKU01000219). The JSpecies program was used for calculating the average nucleotide identity (ANI) value [12] among the 8 strains, which were cut into fragments of 1020 bp for calculating the ANI values by using the BLAST algorithm [13]. Next, a distance dendrogram was constructed using the R program.

Quality assurance

The genomic DNA used for sequencing was isolated from a pure culture of V. campbellii strain 20130629003S01. The 16S rRNA gene was amplified and sequenced, and BLAST was performed against the NCBI database.

Pathogenesis and virulence factors

Key virulence factors in AHPND-causing V. campbellii are pirABvp (pirAvp and pirBvp) [2, 5]. The strain 20130629003S01 harbours four plasmids, pVCGX1, pVCGX2, pVCGX3, and pVCGX4. Interestingly, pVCGX1 has a pirAvp gene and pirBvp gene related to AHPND, and both pirAvp and pirBvp of pVCGX1 share 100% sequence identities with their orthologues in the plasmids pVA1 and pVPA3-1 of Vibrio parahaemolyticus [5, 14]. Therefore, pVCGX1 may contribute to pathogenesis.

Comparative genome analysis

Seven complete reference genome sequences of V. campbellii and their annotations were collected from the GenBank database. The ANI values were calculated using 8 strains, and all values between every two strains were greater than 95%. Furthermore, the 20130629003S01 strain was found to cluster with the LMB29 strain (Fig. 2). The LMB29 strain (GenBank accession number: CP019293.1) was isolated from cage-cultured red drum with skin ulcers in China. Comparative data are shown as a dendrogram in Fig. 2 and tabulated in Additional file 1: Table S1.

Future directions

In conclusion, we report the 5.3 Mbp complete genome sequence of V. campbellii strain 20130629003S01. Additional comparative studies of the genomes of AHPND-causing Vibrio with the genome sequence of strain 20130629003S01 should provide genomic insights into the pathogenicity and virulence mechanisms of VCAHPND.

Author’s contributions

The experiments, data analysis and manuscript writing were performed by XD and JH. HLW isolated and preserved the bacterial strain 20130629003S01. PZZ and JYC performed experiments. ZL performed assembly and annotation sequencing data. XPW discussed the results and revised the manuscript. JH provided the sample for isolation of the strain 20130629003S01, vital guidance, technical support, and proofreading for the work. All authors read and approved the final manuscript.

Acknowledgements

The authors thanks Mr. Daxiang Xie in Guangxi Aquaculture Research Institute and Mr. Debin Pang in Zhengyu Biotechnology Ltd. for their assistance during sampling of the strain 20130629003S01.

Competing interests

The authors declare that they have no competing interests.

Availability of data and materials

The genome sequence of Vibrio campbellii 20130629003S01 has been deposited in NCBI Genbank server under the accession number CP020076–CP020081 for chromosome 1, chromosome 2 and plasmids.

Funding

This work was supported by projects under Central Public-interest Scientific Institution Basal Research Fund, YSFRI, CAFS (20603022016012), the Project of the Aoshan Sci. & Tech. Innovation Program of Qingdao National Laboratory for Marine Science and Technology (2015ASKJ02), the China Agriculture Research System (CARS-47), and the Construction Programme for “Taishan Scholarship” of Shandong Province of China.

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